Code
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestSee the documentation of the MiscMetabar package for example of btea diversity analysis.
Code
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/03_beta_diversity.qmd")
source(here::here("R/styles.R"))Code
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))Cleaning suppress 2 taxa and 1 samples.Code
formattable_pq(
subset_samples(d_pq, Type %in% c("Mix", "Mono")),
factor_of_interest,
min_nb_seq_taxa = 1000,
lev_col_taxa = "Family",
taxonomic_levels=c("Order", "Family", "Genus"),
log10trans = TRUE,
)Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ).Number of non-matching ASV 0Number of matching ASV 1145Number of filtered-out ASV 803Number of kept ASV 342Number of kept samples 437Cleaning suppress 0 taxa and 0 samples.Joining with `by = join_by(OTU)`| OTU | Order | Family | Genus | Mix | Mono | proportion_samp | nb_seq |
|---|---|---|---|---|---|---|---|
| Taxa_2 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 5.71 | 5.89 | 0.84 | 6.11 |
| Taxa_1 | NA | NA | NA | 5.72 | 5.87 | 0.71 | 6.10 |
| Taxa_21 | NA | NA | NA | 5.62 | 5.71 | 0.89 | 5.97 |
| Taxa_3 | Glomerales | Glomeraceae | Glomus | 5.49 | 5.65 | 0.85 | 5.88 |
| Taxa_13 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 5.45 | 5.55 | 0.79 | 5.81 |
| Taxa_11 | Glomerales | Glomeraceae | Glomus | 5.28 | 5.62 | 0.67 | 5.78 |
| Taxa_5 | Glomerales | Glomeraceae | Glomus | 5.42 | 5.48 | 0.81 | 5.75 |
| Taxa_18 | NA | NA | NA | 5.36 | 5.48 | 0.90 | 5.73 |
| Taxa_20 | Glomerales | NA | NA | 5.34 | 5.47 | 0.51 | 5.71 |
| Taxa_12 | Glomerales | Glomeraceae | Glomus | 5.41 | 5.39 | 0.69 | 5.70 |
| Taxa_6 | Glomerales | Glomeraceae | Glomus | 5.23 | 5.53 | 0.80 | 5.70 |
| Taxa_17 | Glomerales | Glomeraceae | Glomus | 5.17 | 5.50 | 0.83 | 5.67 |
| Taxa_7 | Glomerales | Glomeraceae | Glomus | 5.28 | 5.42 | 0.74 | 5.66 |
| Taxa_9 | Glomerales | Glomeraceae | Glomus | 5.26 | 5.42 | 0.65 | 5.65 |
| Taxa_8 | Glomerales | Glomeraceae | Glomus | 5.17 | 5.47 | 0.66 | 5.64 |
| Taxa_10 | Glomerales | Glomeraceae | Glomus | 5.29 | 5.36 | 0.86 | 5.63 |
| Taxa_15 | NA | NA | NA | 5.19 | 5.30 | 0.59 | 5.55 |
| Taxa_14 | Glomerales | Glomeraceae | Glomus | 5.21 | 5.26 | 0.51 | 5.53 |
| Taxa_16 | Glomerales | Glomeraceae | Glomus | 5.14 | 5.27 | 0.66 | 5.51 |
| Taxa_23 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 5.13 | 5.25 | 0.69 | 5.50 |
| Taxa_19 | NA | NA | NA | 5.07 | 5.16 | 0.54 | 5.42 |
| Taxa_36 | Glomerales | Glomeraceae | Glomus | 5.04 | 5.16 | 0.39 | 5.40 |
| Taxa_22 | NA | NA | NA | 4.73 | 5.29 | 0.58 | 5.39 |
| Taxa_27 | NA | NA | NA | 4.97 | 5.15 | 0.95 | 5.37 |
| Taxa_28 | Glomerales | Glomeraceae | Glomus | 4.97 | 5.10 | 0.69 | 5.34 |
| Taxa_24 | Glomerales | Glomeraceae | Glomus | 4.90 | 5.10 | 0.36 | 5.32 |
| Taxa_34 | Glomerales | NA | NA | 4.91 | 5.10 | 0.54 | 5.32 |
| Taxa_41 | Glomerales | Glomeraceae | Glomus | 4.91 | 5.05 | 0.78 | 5.29 |
| Taxa_29 | NA | NA | NA | 4.90 | 5.05 | 0.89 | 5.28 |
| Taxa_30 | NA | NA | NA | 4.88 | 5.07 | 0.75 | 5.28 |
| Taxa_31 | Glomerales | Glomeraceae | Glomus | 4.88 | 5.05 | 0.85 | 5.28 |
| Taxa_32 | Glomerales | NA | NA | 4.87 | 5.04 | 0.92 | 5.26 |
| Taxa_49 | NA | NA | NA | 4.76 | 5.03 | 0.56 | 5.22 |
| Taxa_35 | NA | NA | NA | 4.79 | 5.01 | 0.79 | 5.21 |
| Taxa_48 | Glomerales | NA | NA | 4.76 | 5.00 | 0.48 | 5.20 |
| Taxa_37 | Glomerales | Glomeraceae | Glomus | 4.76 | 4.99 | 0.54 | 5.19 |
| Taxa_38 | NA | NA | NA | 4.82 | 4.91 | 0.75 | 5.17 |
| Taxa_42 | Glomerales | NA | NA | 4.75 | 4.90 | 0.53 | 5.13 |
| Taxa_53 | Glomerales | Glomeraceae | Glomus | 4.82 | 4.74 | 0.55 | 5.08 |
| Taxa_59 | Glomerales | NA | NA | 4.65 | 4.83 | 0.71 | 5.05 |
| Taxa_72 | NA | NA | NA | 4.69 | 4.80 | 0.41 | 5.05 |
| Taxa_45 | Glomerales | Glomeraceae | Glomus | 3.68 | 5.01 | 0.28 | 5.03 |
| Taxa_52 | NA | NA | NA | 4.64 | 4.77 | 0.54 | 5.01 |
| Taxa_97 | Glomerales | Glomeraceae | Glomus | 4.68 | 4.73 | 0.54 | 5.01 |
| Taxa_47 | Glomerales | Glomeraceae | Glomus | 4.53 | 4.80 | 0.71 | 4.99 |
| Taxa_61 | Glomerales | Glomeraceae | NA | 4.60 | 4.75 | 0.49 | 4.98 |
| Taxa_55 | NA | NA | NA | 4.70 | 4.63 | 0.59 | 4.97 |
| Taxa_63 | NA | NA | NA | 4.55 | 4.76 | 0.46 | 4.97 |
| Taxa_51 | Glomerales | Glomeraceae | Glomus | 4.60 | 4.69 | 0.53 | 4.95 |
| Taxa_54 | Glomerales | Glomeraceae | Glomus | 4.56 | 4.66 | 0.43 | 4.91 |
| Taxa_58 | NA | NA | NA | 4.55 | 4.65 | 0.70 | 4.90 |
| Taxa_57 | Glomerales | Glomeraceae | Glomus | 4.54 | 4.62 | 0.24 | 4.89 |
| Taxa_60 | NA | NA | NA | 4.47 | 4.62 | 0.73 | 4.85 |
| Taxa_65 | NA | NA | NA | 4.41 | 4.59 | 0.58 | 4.81 |
| Taxa_113 | NA | NA | NA | 4.37 | 4.59 | 0.42 | 4.80 |
| Taxa_67 | NA | NA | NA | 4.13 | 4.69 | 0.32 | 4.80 |
| Taxa_68 | Glomerales | Glomeraceae | Glomus | 4.56 | 4.43 | 0.24 | 4.80 |
| Taxa_87 | NA | NA | NA | 4.50 | 4.50 | 0.22 | 4.80 |
| Taxa_70 | NA | NA | NA | 4.37 | 4.55 | 0.73 | 4.77 |
| Taxa_66 | NA | NA | NA | 4.43 | 4.49 | 0.41 | 4.76 |
| Taxa_69 | NA | NA | NA | 4.37 | 4.54 | 0.52 | 4.76 |
| Taxa_79 | NA | NA | NA | 4.38 | 4.46 | 0.71 | 4.72 |
| Taxa_73 | NA | NA | NA | 4.31 | 4.46 | 0.57 | 4.69 |
| Taxa_74 | NA | NA | NA | 4.22 | 4.50 | 0.34 | 4.68 |
| Taxa_75 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 4.31 | 4.43 | 0.46 | 4.67 |
| Taxa_81 | Glomerales | NA | NA | 4.31 | 4.41 | 0.41 | 4.66 |
| Taxa_151 | NA | NA | NA | 3.93 | 4.55 | 0.22 | 4.65 |
| Taxa_77 | NA | NA | NA | 4.22 | 4.44 | 0.52 | 4.65 |
| Taxa_99 | Glomerales | NA | NA | 4.30 | 4.38 | 0.77 | 4.64 |
| Taxa_80 | NA | NA | NA | 4.24 | 4.39 | 0.65 | 4.62 |
| Taxa_106 | Glomerales | Glomeraceae | Glomus | 4.24 | 4.37 | 0.35 | 4.61 |
| Taxa_129 | NA | NA | NA | 4.27 | 4.35 | 0.62 | 4.61 |
| Taxa_82 | Glomerales | Glomeraceae | Glomus | 4.16 | 4.39 | 0.33 | 4.60 |
| Taxa_138 | NA | NA | NA | 4.31 | 4.27 | 0.32 | 4.59 |
| Taxa_133 | Glomerales | Glomeraceae | Glomus | 4.22 | 4.33 | 0.29 | 4.58 |
| Taxa_86 | NA | NA | NA | 4.14 | 4.37 | 0.30 | 4.57 |
| Taxa_94 | NA | NA | NA | 4.11 | 4.38 | 0.46 | 4.57 |
| Taxa_110 | NA | NA | NA | 4.17 | 4.33 | 0.43 | 4.56 |
| Taxa_90 | NA | NA | NA | 4.26 | 4.23 | 0.03 | 4.55 |
| Taxa_91 | NA | NA | NA | 4.18 | 4.30 | 0.80 | 4.55 |
| Taxa_128 | NA | NA | NA | 4.22 | 4.25 | 0.45 | 4.54 |
| Taxa_139 | NA | NA | NA | 4.21 | 4.26 | 0.44 | 4.54 |
| Taxa_98 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 4.15 | 4.31 | 0.37 | 4.54 |
| Taxa_92 | Glomerales | Glomeraceae | Glomus | 4.27 | 4.17 | 0.38 | 4.53 |
| Taxa_95 | NA | NA | NA | 4.16 | 4.29 | 0.54 | 4.53 |
| Taxa_102 | NA | NA | NA | 1.63 | 4.51 | 0.01 | 4.51 |
| Taxa_123 | NA | NA | NA | 3.94 | 4.37 | 0.45 | 4.51 |
| Taxa_101 | Glomerales | Glomeraceae | Glomus | 4.10 | 4.28 | 0.35 | 4.50 |
| Taxa_126 | Glomerales | Glomeraceae | Glomus | 4.08 | 4.28 | 0.45 | 4.49 |
| Taxa_239 | Glomerales | Glomeraceae | Glomus | 4.10 | 4.26 | 0.49 | 4.49 |
| Taxa_108 | NA | NA | NA | 4.06 | 4.27 | 0.56 | 4.48 |
| Taxa_145 | NA | NA | NA | 4.11 | 4.24 | 0.41 | 4.48 |
| Taxa_191 | Glomerales | Glomeraceae | Glomus | 4.11 | 4.23 | 0.47 | 4.48 |
| Taxa_109 | NA | NA | NA | 4.08 | 4.22 | 0.35 | 4.46 |
| Taxa_111 | NA | NA | NA | 4.10 | 4.21 | 0.46 | 4.46 |
| Taxa_112 | Glomerales | Glomeraceae | Glomus | 4.03 | 4.25 | 0.30 | 4.45 |
| Taxa_156 | NA | NA | NA | 4.11 | 4.17 | 0.42 | 4.44 |
| Taxa_163 | Glomerales | Glomeraceae | Glomus | 4.09 | 4.15 | 0.52 | 4.43 |
| Taxa_188 | Glomerales | NA | NA | 4.09 | 4.16 | 0.51 | 4.43 |
| Taxa_115 | NA | NA | NA | 4.07 | 4.16 | 0.85 | 4.42 |
| Taxa_120 | Glomerales | Glomeraceae | Glomus | 3.91 | 4.23 | 0.31 | 4.40 |
| Taxa_195 | NA | NA | NA | 4.04 | 4.14 | 0.40 | 4.39 |
| Taxa_233 | Glomerales | Glomeraceae | Glomus | 4.06 | 4.12 | 0.34 | 4.39 |
| Taxa_166 | NA | NA | NA | 3.97 | 4.15 | 0.58 | 4.37 |
| Taxa_137 | Glomerales | Glomeraceae | Glomus | 4.16 | 3.88 | 0.26 | 4.34 |
| Taxa_130 | Glomerales | Glomeraceae | Glomus | 2.37 | 4.32 | 0.08 | 4.32 |
| Taxa_147 | NA | NA | NA | 3.99 | 4.04 | 0.32 | 4.32 |
| Taxa_164 | NA | NA | NA | 3.97 | 4.04 | 0.42 | 4.31 |
| Taxa_132 | Glomerales | Glomeraceae | Glomus | 3.98 | 4.01 | 0.18 | 4.30 |
| Taxa_140 | Glomerales | Glomeraceae | Glomus | 3.94 | 4.02 | 0.46 | 4.28 |
| Taxa_165 | Glomerales | Glomeraceae | Glomus | 3.83 | 4.09 | 0.26 | 4.28 |
| Taxa_184 | NA | NA | NA | 3.85 | 4.09 | 0.37 | 4.28 |
| Taxa_136 | NA | NA | NA | 3.82 | 4.07 | 0.44 | 4.26 |
| Taxa_143 | NA | NA | NA | 3.92 | 3.97 | 0.37 | 4.24 |
| Taxa_148 | NA | NA | NA | 3.81 | 4.04 | 0.35 | 4.24 |
| Taxa_150 | Glomerales | Glomeraceae | Glomus | 3.84 | 3.98 | 0.25 | 4.22 |
| Taxa_153 | NA | NA | NA | 3.70 | 4.02 | 0.28 | 4.19 |
| Taxa_187 | NA | NA | NA | 3.73 | 4.00 | 0.33 | 4.19 |
| Taxa_235 | NA | NA | NA | 3.76 | 3.99 | 0.26 | 4.19 |
| Taxa_157 | NA | NA | NA | 3.62 | 4.04 | 0.25 | 4.18 |
| Taxa_312 | NA | NA | NA | 3.79 | 3.93 | 0.37 | 4.17 |
| Taxa_175 | NA | NA | NA | 3.73 | 3.94 | 0.34 | 4.15 |
| Taxa_204 | Glomerales | Glomeraceae | Glomus | 3.83 | 3.87 | 0.32 | 4.15 |
| Taxa_181 | NA | NA | NA | 3.80 | 3.83 | 0.26 | 4.12 |
| Taxa_176 | Glomerales | Glomeraceae | Glomus | 3.69 | 3.86 | 0.30 | 4.08 |
| Taxa_179 | Glomerales | Glomeraceae | Glomus | 3.87 | 3.67 | 0.12 | 4.08 |
| Taxa_199 | Glomerales | NA | NA | 3.73 | 3.83 | 0.41 | 4.08 |
| Taxa_206 | NA | NA | NA | 3.73 | 3.81 | 0.19 | 4.08 |
| Taxa_264 | NA | NA | NA | 3.59 | 3.91 | 0.22 | 4.08 |
| Taxa_190 | NA | NA | NA | 3.47 | 3.94 | 0.21 | 4.07 |
| Taxa_220 | Glomerales | Glomeraceae | Glomus | 3.63 | 3.87 | 0.14 | 4.07 |
| Taxa_183 | Glomerales | Glomeraceae | Glomus | 3.69 | 3.82 | 0.29 | 4.06 |
| Taxa_185 | NA | NA | NA | 3.72 | 3.80 | 0.37 | 4.06 |
| Taxa_217 | Glomerales | NA | NA | 3.56 | 3.89 | 0.13 | 4.06 |
| Taxa_236 | NA | NA | NA | 3.55 | 3.90 | 0.07 | 4.06 |
| Taxa_259 | NA | NA | NA | 3.66 | 3.84 | 0.33 | 4.06 |
| Taxa_271 | NA | NA | NA | 3.75 | 3.77 | 0.25 | 4.06 |
| Taxa_294 | NA | NA | NA | 3.74 | 3.79 | 0.13 | 4.06 |
| Taxa_192 | Glomerales | NA | NA | 3.69 | 3.80 | 0.27 | 4.05 |
| Taxa_194 | Glomerales | NA | NA | 3.50 | 3.89 | 0.11 | 4.04 |
| Taxa_213 | Glomerales | Glomeraceae | Glomus | 3.56 | 3.86 | 0.15 | 4.04 |
| Taxa_310 | NA | NA | NA | 3.46 | 3.90 | 0.17 | 4.04 |
| Taxa_200 | Glomerales | Glomeraceae | Glomus | 3.63 | 3.79 | 0.28 | 4.02 |
| Taxa_214 | NA | NA | NA | 3.83 | 3.58 | 0.03 | 4.02 |
| Taxa_202 | Glomerales | NA | NA | 3.62 | 3.79 | 0.24 | 4.01 |
| Taxa_205 | Glomerales | Glomeraceae | Glomus | 3.67 | 3.75 | 0.14 | 4.01 |
| Taxa_207 | Glomerales | NA | NA | 3.65 | 3.74 | 0.16 | 4.00 |
| Taxa_234 | NA | NA | NA | 3.36 | 3.88 | 0.19 | 4.00 |
| Taxa_248 | NA | NA | NA | 3.64 | 3.76 | 0.26 | 4.00 |
| Taxa_209 | Glomerales | Glomeraceae | Glomus | 3.23 | 3.91 | 0.20 | 3.99 |
| Taxa_211 | Glomerales | Glomeraceae | Glomus | 3.69 | 3.70 | 0.21 | 3.99 |
| Taxa_212 | Glomerales | Glomeraceae | Glomus | 3.68 | 3.71 | 0.25 | 3.99 |
| Taxa_288 | NA | NA | NA | 3.59 | 3.77 | 0.33 | 3.99 |
| Taxa_229 | NA | NA | NA | 3.64 | 3.70 | 0.29 | 3.97 |
| Taxa_258 | Glomerales | Glomeraceae | Glomus | 3.58 | 3.75 | 0.17 | 3.97 |
| Taxa_222 | Glomerales | NA | NA | 3.56 | 3.73 | 0.28 | 3.96 |
| Taxa_215 | Glomerales | Glomeraceae | Glomus | 3.65 | 3.65 | 0.19 | 3.95 |
| Taxa_223 | Glomerales | Glomeraceae | Glomus | 3.56 | 3.73 | 0.25 | 3.95 |
| Taxa_245 | Glomerales | Glomeraceae | Glomus | 3.56 | 3.71 | 0.42 | 3.94 |
| Taxa_269 | NA | NA | NA | 3.69 | 3.59 | 0.25 | 3.94 |
| Taxa_261 | Glomerales | Glomeraceae | Glomus | 3.55 | 3.67 | 0.18 | 3.92 |
| Taxa_366 | Glomerales | Glomeraceae | Glomus | 3.47 | 3.73 | 0.14 | 3.92 |
| Taxa_257 | NA | NA | NA | 3.58 | 3.60 | 0.15 | 3.89 |
| Taxa_339 | NA | NA | NA | 3.59 | 3.59 | 0.21 | 3.89 |
| Taxa_328 | NA | NA | NA | 2.91 | 3.82 | 0.03 | 3.87 |
| Taxa_228 | NA | NA | NA | 3.48 | 3.60 | 0.29 | 3.85 |
| Taxa_246 | NA | NA | NA | 3.57 | 3.53 | 0.15 | 3.85 |
| Taxa_251 | NA | NA | NA | 3.59 | 3.52 | 0.18 | 3.85 |
| Taxa_252 | Glomerales | NA | NA | 3.52 | 3.57 | 0.35 | 3.85 |
| Taxa_263 | NA | NA | NA | 3.47 | 3.60 | 0.09 | 3.84 |
| Taxa_341 | NA | NA | NA | 3.28 | 3.70 | 0.06 | 3.84 |
| Taxa_253 | Glomerales | Glomeraceae | Glomus | 3.59 | 3.46 | 0.01 | 3.83 |
| Taxa_292 | NA | NA | NA | 3.53 | 3.50 | 0.38 | 3.82 |
| Taxa_322 | Glomerales | Glomeraceae | Glomus | 3.34 | 3.65 | 0.18 | 3.82 |
| Taxa_249 | Glomerales | Glomeraceae | Glomus | 3.10 | 3.72 | 0.04 | 3.81 |
| Taxa_365 | Glomerales | Glomeraceae | Glomus | 3.39 | 3.60 | 0.19 | 3.81 |
| Taxa_293 | NA | NA | NA | 3.48 | 3.51 | 0.19 | 3.80 |
| Taxa_332 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 3.43 | 3.52 | 0.18 | 3.78 |
| Taxa_266 | NA | NA | NA | 3.42 | 3.51 | 0.30 | 3.77 |
| Taxa_276 | NA | NA | NA | 3.26 | 3.60 | 0.22 | 3.77 |
| Taxa_274 | NA | NA | NA | 3.38 | 3.52 | 0.19 | 3.76 |
| Taxa_289 | NA | NA | NA | 3.70 | 2.85 | 0.01 | 3.76 |
| Taxa_278 | Glomerales | NA | NA | 3.28 | 3.57 | 0.04 | 3.75 |
| Taxa_279 | Glomerales | Glomeraceae | Glomus | 3.56 | 3.30 | 0.12 | 3.75 |
| Taxa_349 | NA | NA | NA | 3.15 | 3.63 | 0.06 | 3.75 |
| Taxa_361 | Glomerales | Glomeraceae | Glomus | 3.44 | 3.46 | 0.10 | 3.75 |
| Taxa_323 | NA | NA | NA | 3.25 | 3.58 | 0.11 | 3.74 |
| Taxa_363 | Glomerales | Glomeraceae | Glomus | 3.47 | 3.40 | 0.14 | 3.74 |
| Taxa_285 | NA | NA | NA | 3.37 | 3.48 | 0.18 | 3.73 |
| Taxa_500 | Glomerales | Glomeraceae | Glomus | 3.24 | 3.56 | 0.11 | 3.73 |
| Taxa_354 | NA | NA | NA | 3.43 | 3.40 | 0.05 | 3.72 |
| Taxa_296 | Glomerales | Glomeraceae | Glomus | 3.24 | 3.50 | 0.13 | 3.69 |
| Taxa_301 | NA | NA | NA | 3.40 | 3.35 | 0.17 | 3.68 |
| Taxa_302 | Glomerales | Glomeraceae | Glomus | 3.36 | 3.39 | 0.08 | 3.68 |
| Taxa_313 | NA | NA | NA | 3.16 | 3.52 | 0.17 | 3.68 |
| Taxa_319 | Glomerales | Glomeraceae | Glomus | 3.24 | 3.48 | 0.12 | 3.68 |
| Taxa_304 | NA | NA | NA | 3.54 | 3.11 | 0.08 | 3.67 |
| Taxa_305 | NA | NA | NA | 3.36 | 3.39 | 0.15 | 3.67 |
| Taxa_318 | NA | NA | NA | 3.23 | 3.48 | 0.14 | 3.67 |
| Taxa_309 | NA | NA | NA | 3.30 | 3.42 | 0.10 | 3.66 |
| Taxa_368 | Glomerales | Glomeraceae | Glomus | 3.20 | 3.48 | 0.10 | 3.66 |
| Taxa_389 | Glomerales | Glomeraceae | Glomus | 3.11 | 3.52 | 0.05 | 3.66 |
| Taxa_317 | NA | NA | NA | 2.14 | 3.64 | 0.02 | 3.65 |
| Taxa_345 | NA | NA | NA | 3.27 | 3.41 | 0.16 | 3.65 |
| Taxa_316 | Glomerales | Glomeraceae | Glomus | 3.23 | 3.43 | 0.11 | 3.64 |
| Taxa_396 | Glomerales | NA | NA | 3.20 | 3.43 | 0.29 | 3.63 |
| Taxa_558 | Glomerales | Glomeraceae | Glomus | 3.27 | 3.37 | 0.13 | 3.63 |
| Taxa_329 | NA | NA | NA | 3.28 | 3.34 | 0.08 | 3.61 |
| Taxa_362 | Glomerales | Glomeraceae | Glomus | 3.15 | 3.40 | 0.22 | 3.60 |
| Taxa_370 | NA | NA | NA | 3.26 | 3.35 | 0.16 | 3.60 |
| Taxa_342 | Glomerales | Glomeraceae | Glomus | 3.20 | 3.36 | 0.16 | 3.59 |
| Taxa_337 | Paraglomerales | Paraglomeraceae | Paraglomus | 3.19 | 3.36 | 0.20 | 3.58 |
| Taxa_344 | Glomerales | Glomeraceae | Glomus | 3.21 | 3.31 | 0.14 | 3.57 |
| Taxa_346 | NA | NA | NA | 3.09 | 3.40 | 0.30 | 3.57 |
| Taxa_348 | NA | NA | NA | 3.22 | 3.29 | 0.12 | 3.56 |
| Taxa_357 | NA | NA | NA | 3.49 | 2.67 | 0.05 | 3.55 |
| Taxa_588 | Diversisporales | NA | NA | 3.24 | 3.27 | 0.13 | 3.55 |
| Taxa_352 | NA | NA | NA | 2.03 | 3.53 | 0.04 | 3.54 |
| Taxa_358 | Glomerales | NA | NA | 3.08 | 3.36 | 0.03 | 3.54 |
| Taxa_378 | Glomerales | Glomeraceae | Glomus | 3.20 | 3.25 | 0.30 | 3.53 |
| Taxa_427 | NA | NA | NA | 2.44 | 3.49 | 0.09 | 3.53 |
| Taxa_430 | Glomerales | Glomeraceae | Glomus | 2.71 | 3.45 | 0.05 | 3.52 |
| Taxa_433 | NA | NA | NA | 3.24 | 3.19 | 0.18 | 3.52 |
| Taxa_364 | NA | NA | NA | 3.45 | 2.65 | 0.02 | 3.51 |
| Taxa_376 | NA | NA | NA | 3.21 | 3.20 | 0.15 | 3.51 |
| Taxa_520 | NA | NA | NA | 3.19 | 3.23 | 0.14 | 3.51 |
| Taxa_553 | Glomerales | NA | NA | 1.89 | 3.50 | 0.03 | 3.51 |
| Taxa_367 | NA | NA | NA | 3.09 | 3.29 | 0.28 | 3.50 |
| Taxa_373 | Glomerales | Glomeraceae | Glomus | 3.12 | 3.24 | 0.13 | 3.49 |
| Taxa_404 | Glomerales | Glomeraceae | Glomus | 2.92 | 3.35 | 0.04 | 3.49 |
| Taxa_496 | Glomerales | NA | NA | 3.09 | 3.27 | 0.10 | 3.49 |
| Taxa_559 | Glomerales | Glomeraceae | Glomus | 0.00 | 3.49 | 0.01 | 3.49 |
| Taxa_403 | NA | NA | NA | 3.23 | 3.12 | 0.13 | 3.48 |
| Taxa_420 | NA | NA | NA | 3.20 | 3.15 | 0.15 | 3.48 |
| Taxa_394 | Glomerales | Glomeraceae | Glomus | 3.23 | 3.11 | 0.09 | 3.47 |
| Taxa_424 | NA | NA | NA | 3.04 | 3.26 | 0.07 | 3.47 |
| Taxa_482 | Glomerales | NA | NA | 3.10 | 3.24 | 0.09 | 3.47 |
| Taxa_379 | Glomerales | Glomeraceae | Glomus | 3.15 | 3.16 | 0.30 | 3.46 |
| Taxa_393 | Glomerales | Glomeraceae | Glomus | 3.20 | 3.09 | 0.08 | 3.45 |
| Taxa_390 | NA | NA | NA | 2.75 | 3.34 | 0.07 | 3.44 |
| Taxa_407 | NA | NA | NA | 3.11 | 3.15 | 0.14 | 3.43 |
| Taxa_412 | NA | NA | NA | 3.14 | 3.12 | 0.16 | 3.43 |
| Taxa_402 | NA | NA | NA | 3.12 | 3.11 | 0.19 | 3.42 |
| Taxa_406 | Glomerales | Glomeraceae | Glomus | 3.42 | 0.00 | 0.00 | 3.42 |
| Taxa_527 | NA | NA | NA | 3.02 | 3.20 | 0.07 | 3.42 |
| Taxa_545 | NA | NA | NA | 3.10 | 3.11 | 0.06 | 3.41 |
| Taxa_408 | Glomerales | Glomeraceae | Glomus | 2.52 | 3.34 | 0.06 | 3.40 |
| Taxa_409 | Glomerales | Glomeraceae | Glomus | 2.93 | 3.22 | 0.04 | 3.40 |
| Taxa_418 | NA | NA | NA | 3.32 | 2.62 | 0.01 | 3.40 |
| Taxa_419 | NA | NA | NA | 3.05 | 3.15 | 0.06 | 3.40 |
| Taxa_463 | Glomerales | Glomeraceae | Glomus | 3.12 | 3.07 | 0.06 | 3.40 |
| Taxa_561 | NA | NA | NA | 3.18 | 2.99 | 0.06 | 3.40 |
| Taxa_422 | NA | NA | NA | 2.82 | 3.25 | 0.09 | 3.39 |
| Taxa_648 | NA | NA | NA | 2.83 | 3.19 | 0.07 | 3.35 |
| Taxa_460 | NA | NA | NA | 2.95 | 3.11 | 0.11 | 3.34 |
| Taxa_533 | Glomerales | Glomeraceae | Glomus | 3.01 | 3.07 | 0.08 | 3.34 |
| Taxa_440 | NA | NA | NA | 2.88 | 3.14 | 0.03 | 3.33 |
| Taxa_441 | Glomerales | Glomeraceae | Glomus | 2.78 | 3.18 | 0.08 | 3.33 |
| Taxa_443 | NA | NA | NA | 2.41 | 3.27 | 0.01 | 3.33 |
| Taxa_591 | Glomerales | Glomeraceae | Glomus | 2.95 | 3.10 | 0.08 | 3.33 |
| Taxa_442 | Glomerales | Glomeraceae | Glomus | 3.08 | 2.95 | 0.05 | 3.32 |
| Taxa_715 | NA | NA | NA | 3.09 | 2.93 | 0.06 | 3.32 |
| Taxa_484 | NA | NA | NA | 2.90 | 3.11 | 0.11 | 3.31 |
| Taxa_480 | NA | NA | NA | 2.89 | 3.08 | 0.14 | 3.30 |
| Taxa_556 | Glomerales | Glomeraceae | Glomus | 2.84 | 3.12 | 0.08 | 3.30 |
| Taxa_450 | NA | NA | NA | 3.13 | 2.78 | 0.03 | 3.29 |
| Taxa_453 | NA | NA | NA | 2.78 | 3.13 | 0.05 | 3.29 |
| Taxa_454 | Glomerales | Glomeraceae | Glomus | 3.01 | 2.97 | 0.07 | 3.29 |
| Taxa_459 | Diversisporales | NA | NA | 2.83 | 3.11 | 0.07 | 3.29 |
| Taxa_612 | NA | NA | NA | 2.77 | 3.13 | 0.07 | 3.29 |
| Taxa_462 | Glomerales | Glomeraceae | Glomus | 3.05 | 2.88 | 0.08 | 3.28 |
| Taxa_465 | Glomerales | NA | NA | 2.88 | 3.06 | 0.07 | 3.28 |
| Taxa_532 | NA | NA | NA | 2.78 | 3.10 | 0.25 | 3.27 |
| Taxa_535 | NA | NA | NA | 3.08 | 2.80 | 0.05 | 3.26 |
| Taxa_572 | NA | NA | NA | 2.80 | 3.07 | 0.04 | 3.26 |
| Taxa_759 | NA | NA | NA | 2.85 | 3.05 | 0.13 | 3.26 |
| Taxa_474 | NA | NA | NA | 2.58 | 3.15 | 0.05 | 3.25 |
| Taxa_475 | Glomerales | Glomeraceae | Glomus | 0.00 | 3.25 | 0.00 | 3.25 |
| Taxa_593 | Glomerales | Glomeraceae | Glomus | 2.85 | 3.03 | 0.10 | 3.25 |
| Taxa_510 | NA | NA | NA | 2.82 | 3.03 | 0.06 | 3.24 |
| Taxa_549 | Glomerales | Glomeraceae | Glomus | 2.79 | 3.04 | 0.19 | 3.23 |
| Taxa_554 | Glomerales | NA | NA | 2.93 | 2.93 | 0.05 | 3.23 |
| Taxa_585 | NA | NA | NA | 2.90 | 2.96 | 0.07 | 3.23 |
| Taxa_483 | NA | NA | NA | 2.49 | 3.13 | 0.04 | 3.22 |
| Taxa_485 | NA | NA | NA | 3.11 | 2.54 | 0.03 | 3.21 |
| Taxa_696 | Glomerales | Glomeraceae | Glomus | 2.96 | 2.85 | 0.03 | 3.21 |
| Taxa_489 | NA | NA | NA | 2.97 | 2.82 | 0.07 | 3.20 |
| Taxa_498 | NA | NA | NA | 2.80 | 2.97 | 0.17 | 3.20 |
| Taxa_509 | Glomerales | Glomeraceae | Glomus | 2.97 | 2.82 | 0.07 | 3.20 |
| Taxa_604 | NA | NA | NA | 2.97 | 2.82 | 0.07 | 3.20 |
| Taxa_495 | NA | NA | NA | 2.83 | 2.95 | 0.16 | 3.19 |
| Taxa_632 | NA | NA | NA | 2.90 | 2.87 | 0.11 | 3.19 |
| Taxa_640 | NA | NA | NA | 2.84 | 2.93 | 0.08 | 3.19 |
| Taxa_503 | NA | NA | NA | 2.74 | 2.99 | 0.06 | 3.18 |
| Taxa_512 | Glomerales | Glomeraceae | Glomus | 2.51 | 3.07 | 0.16 | 3.18 |
| Taxa_570 | Glomerales | Glomeraceae | Glomus | 2.68 | 3.02 | 0.08 | 3.18 |
| Taxa_608 | Glomerales | Glomeraceae | Glomus | 2.80 | 2.96 | 0.07 | 3.18 |
| Taxa_1093 | NA | NA | NA | 2.85 | 2.90 | 0.13 | 3.17 |
| Taxa_507 | NA | NA | NA | 2.92 | 2.81 | 0.02 | 3.17 |
| Taxa_511 | NA | NA | NA | 2.93 | 2.80 | 0.07 | 3.17 |
| Taxa_521 | NA | NA | NA | 2.80 | 2.93 | 0.04 | 3.17 |
| Taxa_526 | NA | NA | NA | 0.00 | 3.17 | 0.01 | 3.17 |
| Taxa_551 | Glomerales | Glomeraceae | Glomus | 2.82 | 2.91 | 0.14 | 3.17 |
| Taxa_673 | Glomerales | Glomeraceae | Glomus | 2.57 | 3.04 | 0.09 | 3.17 |
| Taxa_514 | Glomerales | Glomeraceae | Glomus | 2.81 | 2.92 | 0.03 | 3.16 |
| Taxa_626 | Glomerales | NA | NA | 2.82 | 2.91 | 0.09 | 3.16 |
| Taxa_586 | NA | NA | NA | 2.80 | 2.89 | 0.08 | 3.15 |
| Taxa_672 | Glomerales | Glomeraceae | Glomus | 2.59 | 3.02 | 0.05 | 3.15 |
| Taxa_625 | Glomerales | Glomeraceae | Glomus | 2.82 | 2.85 | 0.09 | 3.14 |
| Taxa_659 | NA | NA | NA | 2.70 | 2.94 | 0.08 | 3.14 |
| Taxa_660 | NA | NA | NA | 2.74 | 2.93 | 0.05 | 3.14 |
| Taxa_541 | Glomerales | NA | NA | 2.98 | 2.60 | 0.07 | 3.13 |
| Taxa_557 | NA | NA | NA | 2.26 | 3.05 | 0.05 | 3.12 |
| Taxa_569 | Glomerales | Glomeraceae | Glomus | 0.00 | 3.12 | 0.01 | 3.12 |
| Taxa_631 | Glomerales | Glomeraceae | Glomus | 2.62 | 2.96 | 0.05 | 3.12 |
| Taxa_1041 | NA | NA | NA | 2.77 | 2.85 | 0.05 | 3.11 |
| Taxa_540 | Glomerales | Glomeraceae | Glomus | 3.01 | 2.40 | 0.01 | 3.11 |
| Taxa_547 | NA | NA | NA | 2.67 | 2.91 | 0.10 | 3.11 |
| Taxa_564 | Glomerales | NA | NA | 3.09 | 1.71 | 0.01 | 3.10 |
| Taxa_597 | NA | NA | NA | 2.89 | 2.67 | 0.08 | 3.10 |
| Taxa_600 | NA | NA | NA | 2.57 | 2.96 | 0.09 | 3.10 |
| Taxa_571 | Glomerales | Glomeraceae | Glomus | 3.09 | 0.00 | 0.00 | 3.09 |
| Taxa_574 | NA | NA | NA | 2.77 | 2.81 | 0.07 | 3.09 |
| Taxa_596 | NA | NA | NA | 2.82 | 2.76 | 0.02 | 3.09 |
| Taxa_598 | Glomerales | NA | NA | 2.20 | 3.02 | 0.04 | 3.08 |
| Taxa_583 | Glomerales | Glomeraceae | Glomus | 2.82 | 2.71 | 0.07 | 3.07 |
| Taxa_850 | NA | NA | NA | 2.57 | 2.91 | 0.25 | 3.07 |
| Taxa_594 | Glomerales | Glomeraceae | Glomus | 2.66 | 2.84 | 0.07 | 3.06 |
| Taxa_603 | NA | NA | NA | 2.81 | 2.71 | 0.03 | 3.06 |
| Taxa_599 | NA | NA | NA | 2.62 | 2.85 | 0.07 | 3.05 |
| Taxa_729 | NA | NA | NA | 2.59 | 2.86 | 0.10 | 3.05 |
| Taxa_605 | NA | NA | NA | 2.71 | 2.77 | 0.04 | 3.04 |
| Taxa_610 | NA | NA | NA | 0.00 | 3.03 | 0.00 | 3.03 |
| Taxa_611 | Glomerales | Glomeraceae | Glomus | 2.68 | 2.78 | 0.07 | 3.03 |
| Taxa_613 | Glomerales | Glomeraceae | Glomus | 0.00 | 3.03 | 0.00 | 3.03 |
| Taxa_615 | NA | NA | NA | 2.73 | 2.73 | 0.06 | 3.03 |
| Taxa_733 | NA | NA | NA | 2.60 | 2.83 | 0.18 | 3.03 |
| Taxa_619 | Glomerales | Glomeraceae | Glomus | 2.72 | 2.72 | 0.03 | 3.02 |
| Taxa_624 | Glomerales | Claroideoglomeraceae | Claroideoglomus | 2.43 | 2.88 | 0.04 | 3.01 |
| Taxa_687 | Glomerales | Glomeraceae | Glomus | 3.01 | 0.00 | 0.00 | 3.01 |
| Taxa_679 | NA | NA | NA | 2.64 | 2.76 | 0.12 | 3.00 |
| Taxa_867 | NA | NA | NA | 2.31 | 2.91 | 0.04 | 3.00 |
Code
library("vegan")Le chargement a nécessité le package : permuteLe chargement a nécessité le package : latticeThis is vegan 2.6-8Code
plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), "matrix"),
method = "robust.aitchison"
)), color = factor_of_interest) +
geom_point(size = 3) +
stat_ellipse(inherit.aes = F, aes(x = DCA1, y = DCA2, linetype = .data[[factor_of_interest]], col = .data[[factor_of_interest]])) + theme_idest() + scale_color_manual(values=idest_pal$dark_color_idest[[1]][c(5,4,2)])Warning in plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), :
`Ordination species/OTU/taxa coordinate indices did not match `physeq` index
names. Setting corresponding coordinates to NULL.Too few points to calculate an ellipseToo few points to calculate an ellipseWarning: Removed 2 rows containing missing values or values outside the scale range
(`geom_path()`).
Code
adonis_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, na_remove = TRUE, correction_for_sample_size = TRUE, by = "terms")TypePermutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
vegan::adonis2(formula = .formula, data = metadata, by = "terms")
Df SumOfSqs R2 F Pr(>F)
sample_size 1 8.279 0.06740 31.4270 0.001 ***
Type 1 0.225 0.00183 0.8532 0.573
Residual 434 114.326 0.93077
Total 436 122.829 1.00000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Code
d_pq |>
subset_samples(Type %in% c("Mix", "Mono")) |>
biplot_pq(merge_sample_by = factor_of_interest, rarefy_after_merging = T)Cleaning suppress 2 taxa and 0 samples.You set `rngseed` to FALSE. Make sure you've set & recorded
the random seed of your session for reproducibility.
See `?set.seed`...9OTUs were removed because they are no longer
present in any sample after random subsampling...Cleaning suppress 0 taxa and 0 samples.Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
res_var <- var_par_rarperm_pq( subset_samples(d_pq, Type %in% c(“Mix”, “Mono”)), list_component = list( “Tmt” = c(“Tmt”), “Bloc” = c(“Bloc”), “Type” = c(“Type”) ), nperm = 9, dbrda_computation = TRUE )
plot_var_part_pq(res_var)
## Session Information
Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file <a href="data_final/information_run.txt" title="Download the informations about the hardwares and softwfares used to run these analysis" class="inline-btn"> data_final/information_run.txt </a>.
<button style="width:100%" type="button" data-bs-toggle="collapse" data-bs-target="#collapseOne" class="button-collapse">
Session Information
</button>
:::: {#collapseOne .accordion-collapse .collapse}
<div>
::: {.cell}
```{.r .cell-code}
sessionInfo()
```
::: {.cell-output .cell-output-stdout}
```
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] vegan_2.6-8 lattice_0.22-6 permute_0.9-7 MiscMetabar_0.10.1
[5] purrr_1.0.2 dplyr_1.1.4 dada2_1.32.0 Rcpp_1.0.13
[9] ggplot2_3.5.1 phyloseq_1.48.0 targets_1.8.0 knitr_1.48
loaded via a namespace (and not attached):
[1] bitops_1.0-9 deldir_2.0-4
[3] gridExtra_2.3 rlang_1.1.4
[5] magrittr_2.0.3 ade4_1.7-22
[7] matrixStats_1.4.1 compiler_4.4.1
[9] mgcv_1.9-1 png_0.1-8
[11] callr_3.7.6 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1
[15] pwalign_1.0.0 pkgconfig_2.0.3
[17] crayon_1.5.3 fastmap_1.2.0
[19] backports_1.5.0 XVector_0.44.0
[21] labeling_0.4.3 utf8_1.2.4
[23] Rsamtools_2.20.0 rmarkdown_2.28
[25] UCSC.utils_1.0.0 ps_1.8.0
[27] xfun_0.48 zlibbioc_1.50.0
[29] GenomeInfoDb_1.40.1 jsonlite_1.8.9
[31] biomformat_1.32.0 rhdf5filters_1.16.0
[33] DelayedArray_0.30.1 Rhdf5lib_1.26.0
[35] BiocParallel_1.38.0 jpeg_0.1-10
[37] parallel_4.4.1 cluster_2.1.6
[39] R6_2.5.1 RColorBrewer_1.1-3
[41] stringi_1.8.4 GenomicRanges_1.56.2
[43] SummarizedExperiment_1.34.0 iterators_1.0.14
[45] IRanges_2.38.1 Matrix_1.7-0
[47] splines_4.4.1 igraph_2.1.1
[49] tidyselect_1.2.1 viridis_0.6.5
[51] abind_1.4-8 yaml_2.3.10
[53] codetools_0.2-20 hwriter_1.3.2.1
[55] processx_3.8.4 tibble_3.2.1
[57] plyr_1.8.9 Biobase_2.64.0
[59] withr_3.0.1 ShortRead_1.62.0
[61] evaluate_1.0.1 survival_3.7-0
[63] RcppParallel_5.1.9 formattable_0.2.1
[65] Biostrings_2.72.1 pillar_1.9.0
[67] BiocManager_1.30.25 MatrixGenerics_1.16.0
[69] renv_1.0.11 foreach_1.5.2
[71] stats4_4.4.1 generics_0.1.3
[73] rprojroot_2.0.4 S4Vectors_0.42.1
[75] munsell_0.5.1 scales_1.3.0
[77] base64url_1.4 glue_1.8.0
[79] tools_4.4.1 interp_1.1-6
[81] data.table_1.16.2 GenomicAlignments_1.40.0
[83] rhdf5_2.48.0 grid_4.4.1
[85] tidyr_1.3.1 ape_5.8
[87] latticeExtra_0.6-30 colorspace_2.1-1
[89] nlme_3.1-165 GenomeInfoDbData_1.2.12
[91] cli_3.6.3 fansi_1.0.6
[93] viridisLite_0.4.2 S4Arrays_1.4.1
[95] gtable_0.3.5 digest_0.6.37
[97] BiocGenerics_0.50.0 SparseArray_1.4.8
[99] farver_2.1.2 htmlwidgets_1.6.4
[101] htmltools_0.5.8.1 multtest_2.60.0
[103] lifecycle_1.0.4 here_1.0.1
[105] httr_1.4.7 secretbase_1.0.3
[107] MASS_7.3-61
```
:::
:::
</div>
::::
:::{#quarto-navigation-envelope .hidden}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-int-sidebar-title"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-int-navbar-title"}
:::
:::{#quarto-meta-markdown .hidden}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-metatitle"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-twittercardtitle"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-ogcardtitle"}
[Where we analyse the effect of a factor on shared diversity]{.hidden .quarto-markdown-envelope-contents render-id="quarto-twittercarddesc"}
[Where we analyse the effect of a factor on shared diversity]{.hidden .quarto-markdown-envelope-contents render-id="quarto-ogcardddesc"}
:::
<!-- -->
::: {.quarto-embedded-source-code}
```````````````````{.markdown shortcodes="false"}
---
title: "Beta-diversity analysis"
subtitle: "Where we analyse the effect of a factor on shared diversity"
date: last-modified
author:
- name: Adrien Taudière
url: https://adrientaudiere.github.io/bioinfo.starter/analysis/02_alpha_diversity.qmd
affiliation: IdEst
affiliation-url: https://orcid.org/my-orcid?orcid=0000-0003-1088-1182
citation: true
params:
factor_of_interest: "Type"
# bibliography: bibliography.bib
# link-citations: true
---
See the documentation of the `MiscMetabar` package for example of [btea diversity analysis](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html).
quarto-executable-code-5450563D
```r
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interest
```
```{r, message=FALSE, warning=FALSE}
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/03_beta_diversity.qmd")
source(here::here("R/styles.R"))
```
quarto-executable-code-5450563D
```r
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
```
quarto-executable-code-5450563D
```r
#| error: true
formattable_pq(
subset_samples(d_pq, Type %in% c("Mix", "Mono")),
factor_of_interest,
min_nb_seq_taxa = 1000,
lev_col_taxa = "Family",
taxonomic_levels=c("Order", "Family", "Genus"),
log10trans = TRUE,
)
```
quarto-executable-code-5450563D
```r
library("vegan")
plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), "matrix"),
method = "robust.aitchison"
)), color = factor_of_interest) +
geom_point(size = 3) +
stat_ellipse(inherit.aes = F, aes(x = DCA1, y = DCA2, linetype = .data[[factor_of_interest]], col = .data[[factor_of_interest]])) + theme_idest() + scale_color_manual(values=idest_pal$dark_color_idest[[1]][c(5,4,2)])
```
quarto-executable-code-5450563D
```r
adonis_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, na_remove = TRUE, correction_for_sample_size = TRUE, by = "terms")
```
quarto-executable-code-5450563D
```r
d_pq |>
subset_samples(Type %in% c("Mix", "Mono")) |>
biplot_pq(merge_sample_by = factor_of_interest, rarefy_after_merging = T)
```
quarto-executable-code-5450563D
```r
res_var <- var_par_rarperm_pq(
subset_samples(d_pq, Type %in% c("Mix", "Mono")),
list_component = list(
"Tmt" = c("Tmt"),
"Bloc" = c("Bloc"),
"Type" = c("Type")
),
nperm = 9,
dbrda_computation = TRUE
)
plot_var_part_pq(res_var){{< include _session_info.qmd >}} ``````````````````` :::